Examples with Location loci.common.Location used on opensource projects

Example 96 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class FilePattern method findSeriesPatterns.

/**
 * Works like {@link #findSeriesPatterns(String, String, String[])},
 * but dir and nameList are inferred from the given file's absolute
 * path.
 *
 * @param base The file basename to use as a template for the match.
 * @return an array containing all identified patterns.
 */
public static String[] findSeriesPatterns(String base) {
    Location file = new Location(base).getAbsoluteFile();
    Location parent = file.getParentFile();
    String[] list = parent.list(true);
    return findSeriesPatterns(base, parent.getAbsolutePath(), list);
}

Example 97 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class FilePattern method buildFiles.

// -- Helper methods --
// recursive method for building the list of matching filenames
private void buildFiles(String prefix, int ndx, List<String> fileList) {
    if (blocks.length == 0) {
        if (new Location(pattern).exists()) {
            fileList.add(pattern);
            return;
        }
        isRegex = true;
        String[] files = null;
        String dir;
        int endRegex = pattern.indexOf(File.separator + "\\E") + 1;
        int endNotRegex = pattern.lastIndexOf(File.separator) + 1;
        int end;
        // Check if an escaped path has been defined as part of the regex.
        if (pattern.startsWith("\\Q") && endRegex > 0 && endRegex <= endNotRegex) {
            dir = pattern.substring(2, endRegex);
            end = endRegex + 2;
        } else {
            dir = pattern.substring(0, endNotRegex);
            end = endNotRegex;
        }
        if (dir.equals("") || !new Location(dir).exists()) {
            files = Location.getIdMap().keySet().toArray(new String[0]);
            if (files.length == 0) {
                dir = ".";
                files = getAllFiles(dir);
            }
        } else {
            files = getAllFiles(dir);
        }
        Arrays.sort(files);
        String basePattern = pattern.substring(end);
        Pattern regex = null;
        try {
            regex = Pattern.compile(basePattern);
        } catch (PatternSyntaxException e) {
            regex = Pattern.compile(pattern);
        }
        for (String f : files) {
            Location path = new Location(dir, f);
            if (regex.matcher(path.getName()).matches()) {
                if (path.exists())
                    fileList.add(path.getAbsolutePath());
                else
                    fileList.add(f);
            }
        }
    } else {
        // compute bounds for constant (non-block) pattern fragment
        int num = startIndex.length;
        int n1 = ndx == 0 ? 0 : endIndex[ndx - 1];
        int n2 = ndx == num ? pattern.length() : startIndex[ndx];
        String pre = pattern.substring(n1, n2);
        if (ndx == 0)
            fileList.add(pre + prefix);
        else {
            FilePatternBlock block = blocks[--ndx];
            String[] blockElements = block.getElements();
            for (String element : blockElements) {
                buildFiles(element + pre + prefix, ndx, fileList);
            }
        }
    }
}

Example 98 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class FilePattern method getAllFiles.

private String[] getAllFiles(String dir) {
    ArrayList<String> files = new ArrayList<String>();
    Location root = new Location(dir);
    String[] children = root.list();
    for (String child : children) {
        Location file = new Location(root, child);
        if (file.isDirectory()) {
            String[] grandchildren = getAllFiles(file.getAbsolutePath());
            for (String g : grandchildren) {
                files.add(g);
            }
        } else {
            files.add(file.getAbsolutePath());
        }
    }
    return files.toArray(new String[files.size()]);
}

Example 99 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class FileStitcher method getUsedFiles.

/* @see IFormatReader#getUsedFiles() */
@Override
public String[] getUsedFiles() {
    FormatTools.assertId(getCurrentFile(), true, 2);
    if (noStitch)
        return reader.getUsedFiles();
    // returning the files list directly here is fast, since we do not
    // have to call initFile on each constituent file; but we can only do so
    // when each constituent file does not itself have multiple used files
    Set<String> files = new LinkedHashSet<String>();
    for (ExternalSeries s : externals) {
        String[] f = s.getFiles();
        for (String file : f) {
            String path = new Location(file).getAbsolutePath();
            files.add(path);
        }
        DimensionSwapper[] readers = s.getReaders();
        for (int i = 0; i < readers.length; i++) {
            try {
                readers[i].setId(f[i]);
                String[] used = readers[i].getUsedFiles();
                for (String file : used) {
                    String path = new Location(file).getAbsolutePath();
                    files.add(path);
                }
                readers[i].close();
            } catch (FormatException e) {
                LOGGER.debug("", e);
            } catch (IOException e) {
                LOGGER.debug("", e);
            }
        }
    }
    return files.toArray(new String[files.size()]);
}

Example 100 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class Memoizer method setId.

// -- ReaderWrapper API methods --
@Override
public void setId(String id) throws FormatException, IOException {
    StopWatch sw = stopWatch();
    try {
        realFile = new Location(id);
        memoFile = getMemoFile(id);
        if (memoFile == null) {
            // Memoization disabled.
            if (userMetadataStore != null) {
                reader.setMetadataStore(userMetadataStore);
            }
            // EARLY EXIT
            super.setId(id);
            return;
        }
        // Should never throw kryo exceptions
        IFormatReader memo = loadMemo();
        loadedFromMemo = false;
        savedToMemo = false;
        if (memo != null) {
            // loadMemo has already called handleMetadataStore with non-null
            try {
                loadedFromMemo = true;
                reader = memo;
                reader.reopenFile();
            } catch (FileNotFoundException e) {
                LOGGER.info("could not reopen file - deleting invalid memo file: {}", memoFile);
                deleteQuietly(memoFile);
                memo = null;
                reader.close();
                loadedFromMemo = false;
            }
        }
        if (memo == null) {
            OMEXMLService service = getService();
            super.setMetadataStore(service.createOMEXMLMetadata());
            long start = System.currentTimeMillis();
            super.setId(id);
            long elapsed = System.currentTimeMillis() - start;
            // Between setId and saveMemo
            handleMetadataStore(null);
            if (elapsed < minimumElapsed) {
                LOGGER.debug("skipping save memo. elapsed millis: {}", elapsed);
                // EARLY EXIT!
                return;
            }
            // Should never throw.
            savedToMemo = saveMemo();
        }
    } catch (ServiceException e) {
        LOGGER.error("Could not create OMEXMLMetadata", e);
    } finally {
        sw.stop("loci.formats.Memoizer.setId");
    }
}